StyleR run

extract.R

@@ -1,16 +1,20 @@
-#R script to upload the existing spreadsheets and homologise them
+# R script to upload the existing spreadsheets and homologise them
 library(magrittr)
-fList <- list.files("data", pattern="*.xlsx")
+fList <- list.files("data", pattern = "*.xlsx")
 
-#Objective to create data tables with
+# Objective to create data tables with
 linkCheck <- function(nodeType, nodeString, nodeStringCheck) {
   nodeString <- stringr::str_replace_all(nodeString, "\\.", " ")
-  res <- sapply(nodeString, match, nodeStringCheck$Nodes) %>% is.na() %>% which()
-  if (length(res)>0) print(paste("Clean up error found in", nodeType,  "mapping at", names(res)))
+  res <- sapply(nodeString, match, nodeStringCheck$Nodes) %>%
+    is.na() %>%
+    which()
+  if (length(res) > 0) print(paste("Clean up error found in", nodeType, "mapping at", names(res)))
 }
 
 getNodeVals <- function(nodeStr) {
-  params <- stringr::str_split(nodeStr, ",") %>% unlist() %>% trimws()
+  params <- stringr::str_split(nodeStr, ",") %>%
+    unlist() %>%
+    trimws()
   paramVals <- stringr::str_split(params, "=")
   vals <- c()
   lapply(paramVals, function(l) {
@@ -21,18 +25,20 @@ getNodeVals <- function(nodeStr) {
   vals
 }
 
-#We want to build a node table and an impact table.
-#Colnames of the node table will be
-#Hab,  Node Type, Node, Node Layer, Growth,  ....
+# We want to build a node table and an impact table.
+# Colnames of the node table will be
+# Hab,  Node Type, Node, Node Layer, Growth,  ....
 
-#The edges table will be
-#Hab, In Node, Out Node, Params, ....
+# The edges table will be
+# Hab, In Node, Out Node, Params, ....
 
 
 sheetNames <- c("TestScenario", "Map_P_BA", "Map_BA_OP", "Map_OP_ES", "Legend")
 
 cleanNames <- function(namVec) {
-  stringr::str_replace_all(namVec, "\\.", " ") %>% trimws() %>% tolower()
+  stringr::str_replace_all(namVec, "\\.", " ") %>%
+    trimws() %>%
+    tolower()
 }
 
 nodeTable <- tibble::tibble()
@@ -40,43 +46,43 @@ nodeTable <- tibble::tibble()
 for (wbIdx in 1:length(fList)) {
   wb <- openxlsx::loadWorkbook(paste0("data/", fList[wbIdx]))
   hab <- stringr::str_split(fList[wbIdx], "\\.")[[1]][1]
-  #get pressure names
+  # get pressure names
 
-  #Drop the time column no use at all....
-  sheet <- openxlsx::readWorkbook(wb, sheet=sheetNames[1])[ ,-1]
+  # Drop the time column no use at all....
+  sheet <- openxlsx::readWorkbook(wb, sheet = sheetNames[1])[, -1]
   pressures <- cleanNames(colnames(sheet))
-  pressure_nodes <- sheet[1,]
+  pressure_nodes <- sheet[1, ]
 
 
-  sheet <- openxlsx::readWorkbook(wb, sheet=sheetNames[2])[ ,-1]
-  pressure_check <- na.omit(sheet[,1:2])
-  sheet2 <- na.omit(sheet[, -c(1,2)])
+  sheet <- openxlsx::readWorkbook(wb, sheet = sheetNames[2])[, -1]
+  pressure_check <- na.omit(sheet[, 1:2])
+  sheet2 <- na.omit(sheet[, -c(1, 2)])
   ba <- cleanNames(colnames(sheet2))
-  ba_nodes <- sheet2[1,]
-  pressImpact <- sheet2[-1,]
+  ba_nodes <- sheet2[1, ]
+  pressImpact <- sheet2[-1, ]
 
-  #linkCheck("pressures", pressures, pressure_check)
+  # linkCheck("pressures", pressures, pressure_check)
 
 
-  sheet <- openxlsx::readWorkbook(wb, sheet=sheetNames[3])[ ,-1]
-  ba_check <- na.omit(sheet[,1:2])
-  sheet2 <- na.omit(sheet[, -c(1,2)])
+  sheet <- openxlsx::readWorkbook(wb, sheet = sheetNames[3])[, -1]
+  ba_check <- na.omit(sheet[, 1:2])
+  sheet2 <- na.omit(sheet[, -c(1, 2)])
   op <- cleanNames(colnames(sheet2))
-  op_nodes <- sheet2[1,]
-  baImpact <-  sheet2[-1,]
+  op_nodes <- sheet2[1, ]
+  baImpact <- sheet2[-1, ]
 
-  #linkCheck("bioassemblages", ba, ba_check)
+  # linkCheck("bioassemblages", ba, ba_check)
 
-  sheet <- openxlsx::readWorkbook(wb, sheet=sheetNames[4])[ ,-1]
-  op_check <- na.omit(sheet[,1:2])
-  sheet2 <- na.omit(sheet[, -c(1,2)])
+  sheet <- openxlsx::readWorkbook(wb, sheet = sheetNames[4])[, -1]
+  op_check <- na.omit(sheet[, 1:2])
+  sheet2 <- na.omit(sheet[, -c(1, 2)])
   es <- cleanNames(colnames(sheet2))
-  es_nodes <- sheet2[1,]
-  opImpact <-  sheet2[-1,]
+  es_nodes <- sheet2[1, ]
+  opImpact <- sheet2[-1, ]
 
-  #linkCheck("outputprocesses", op, op_check)
+  # linkCheck("outputprocesses", op, op_check)
 
-  legend <- openxlsx::readWorkbook(wb, sheet=sheetNames[5])
+  legend <- openxlsx::readWorkbook(wb, sheet = sheetNames[5])
 
   nodeType <- c(
     rep("pressure", length(pressures)),
@@ -87,25 +93,21 @@ for (wbIdx in 1:length(fList)) {
 
 
 
-  res <- t(sapply(es_nodes[1,], getNodeVals)) %>% as.data.frame()
+  res <- t(sapply(es_nodes[1, ], getNodeVals)) %>% as.data.frame()
   names(res) <- cleanNames(names(res))
-  res <- res %>% mutate(nodeName=names(res))
+  res <- res %>% mutate(nodeName = names(res))
 
   nodeTable <- nodeTable %>% dplyr::bind_rows(
     tibble::tibble(
-      hab=hab,
-      nodeType=nodeType,
+      hab = hab,
+      nodeType = nodeType,
       res
     )
   )
-
 }
 
 mapNewNames <- function() {
   newNameMap <- openxlsx::read.xlsx("MBA_MESO_Nodes.xlsx") %>%
-     dplyr::select(hab, nodeType, Suggestion, node, newname)
-  save(newNameMap, file="nameMap.RData")
+    dplyr::select(hab, nodeType, Suggestion, node, newname)
+  save(newNameMap, file = "nameMap.RData")
 }
-
-
-